Receptor
PDB id Resolution Class Description Source Keywords
1RKG 1.9 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND BINDI COMPLEXED WITH 2MBISP AND A SYNTHETIC PEPTIDE CONTAINING THO F DRIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-LIGAND COMPLEX NUCLEAR RECEPTOR-COACTIVATOINTERACTIONS HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Ref.: MOLECULAR STRUCTURE OF THE RAT VITAMIN D RECEPTOR L BINDING DOMAIN COMPLEXED WITH 2-CARBON-SUBSTITUTED D(3) HORMONE ANALOGUES AND A LXXLL-CONTAINING COACT PEPTIDE BIOCHEMISTRY V. 43 4101 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VD1 A:500;
Valid;
none;
submit data
344.531 C23 H36 O2 CC[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2O4J 1.74 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR LIGAND BINDING D COMPLEXED WITH VITIII 17-20Z AND THE NR2 BOX OF DRIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-LIGAND COMPLEX HORMONE-GROWTH FACTOR RECEPCOMPLEX
Ref.: NEW ANALOGS OF 2-METHYLENE-19-NOR-(20S)-1,25-DIHYDROXYVITAMIN D(3) CONFORMATIONALLY RESTRICTED SIDE CHAINS: EVALUATION BIOLOGICAL ACTIVITY AND STRUCTURAL DETERMINATION OF VDR-BOUND CONFORMATIONS. ARCH.BIOCHEM.BIOPHYS. V. 460 161 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
2 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
3 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
4 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
5 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
6 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
70% Homology Family (56)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 6JEZ - YSV C27 H44 O3 C[C@H](CCC....
6 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
7 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
8 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
9 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
10 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
11 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
12 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
13 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
14 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
15 5B41 - YSV C27 H44 O3 C[C@H](CCC....
16 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
17 6K5O - D0O C25 H42 O5 S C[C@H](CCC....
18 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
19 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
20 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
21 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
22 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
23 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
24 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
25 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
26 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
27 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
28 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
29 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
30 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
31 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
32 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
33 3W5R - LOA C26 H42 O4 C[C@H](CCC....
34 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
35 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
36 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
37 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
38 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
39 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
40 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
41 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
42 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
43 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
44 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
45 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
46 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
47 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
48 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
49 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
50 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
51 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
52 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
53 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
54 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
55 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
56 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
50% Homology Family (56)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 6JEZ - YSV C27 H44 O3 C[C@H](CCC....
6 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
7 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
8 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
9 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
10 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
11 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
12 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
13 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
14 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
15 5B41 - YSV C27 H44 O3 C[C@H](CCC....
16 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
17 6K5O - D0O C25 H42 O5 S C[C@H](CCC....
18 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
19 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
20 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
21 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
22 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
23 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
24 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
25 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
26 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
27 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
28 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
29 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
30 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
31 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
32 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
33 3W5R - LOA C26 H42 O4 C[C@H](CCC....
34 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
35 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
36 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
37 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
38 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
39 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
40 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
41 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
42 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
43 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
44 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
45 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
46 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
47 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
48 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
49 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
50 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
51 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
52 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
53 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
54 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
55 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
56 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VD1; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 VD1 1 1
2 YS2 0.756757 0.863636
3 YS3 0.746667 0.926829
4 YSD 0.74026 0.975
5 YSV 0.717949 0.904762
6 VDZ 0.717949 0.904762
7 8BL 0.633333 0.863636
8 TKA 0.629214 0.904762
9 YA1 0.627907 0.928571
10 8BO 0.626374 0.844444
11 9RO 0.626374 0.844444
12 AKX 0.619565 0.883721
13 YSL 0.609195 0.886364
14 TK3 0.602151 0.904762
15 9KX 0.6 0.902439
16 YS5 0.588889 0.951219
17 YA2 0.588889 0.951219
18 NYA 0.586207 0.902439
19 9N9 0.579545 0.880952
20 TT2 0.569892 0.926829
21 TX5 0.552941 0.857143
22 8C9 0.55102 0.886364
23 MI4 0.541667 0.926829
24 8C0 0.534653 0.866667
25 VD2 0.522727 0.880952
26 VD3 0.488636 0.804878
27 VDY 0.472527 0.878049
28 YW2 0.463918 0.837209
29 VDX 0.463158 0.904762
30 TEJ 0.444444 0.844444
31 MVD 0.438776 0.904762
32 C33 0.431373 0.928571
33 M7E 0.424528 0.666667
34 C3O 0.423077 0.847826
35 8J0 0.419048 0.904762
36 8J3 0.419048 0.904762
37 VD4 0.414894 0.904762
38 VD5 0.414894 0.904762
39 O1C 0.413462 0.844444
40 JC1 0.41 0.886364
41 H97 0.403846 0.770833
42 G72 0.403846 0.770833
43 7ZU 0.402062 0.902439
44 MC9 0.402062 0.902439
45 FMV 0.401961 0.787234
46 OCC 0.401869 0.791667
47 ZNE 0.4 0.716981
Similar Ligands (3D)
Ligand no: 1; Ligand: VD1; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2o4j.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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